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GSE67402: E.coli regulatory changes under long-term starvation

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Results for GadE

Z-value: 1.42

Transcription factors associated with GadE

Gene Symbol Gene ID Gene Info
gadE
gadE DNA-binding transcriptional activator GadE

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
gadE0.617.8e-04Click!

Activity profile of GadE motif

Sorted Z-values of GadE motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
lrp 45.59
lrp
Lrp transcriptional dual regulator
skp-lpxD-fabZ-lpxA 25.61
lpxA
lpxD
skp
fabZ
UDP-N-acetylglucosamine acyltransferase
UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase
periplasmic chaperone
3-hydroxy-acyl-[acyl-carrier-protein] dehydratase
gltBDF 25.14
gltB
gltD
gltF
glutamate synthase, large subunit
glutamate synthase, small subunit
periplasmic protein
purA 14.32
purA
adenylosuccinate synthetase
gnd 13.09
gnd
6-phosphogluconate dehydrogenase, decarboxylating
cyoABCDE 10.98
cyoA
cyoC
cyoB
cyoE
cyoD
cytochrome bo terminal oxidase subunit II
cytochrome bo terminal oxidase subunit III
cytochrome bo terminal oxidase subunit I
heme O synthase
cytochrome bo terminal oxidase subunit IV
gadE-mdtEF 4.64
mdtF
mdtE
gadE
MdtEF-TolC multidrug efflux pump - permease subunit
MdtEF-TolC multidrug efflux pump - membrane fusion protein
GadE DNA-binding transcriptional activator
hdeAB-yhiD 2.09
yhiD
hdeB
hdeA
inner membrane protein YhiD
HdeB monomer
HdeA monomer, chaperone active form
gadXW 0.12
gadW
gadX
GadW DNA-binding transcriptional dual regulator
GadX DNA-binding transcriptional dual regulator

Network of associatons between targets according to the STRING database.

First level regulatory network of GadE

PNG image of the network

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target  Total log-likelihood Term Description
9.1 45.6 GO:0009078 alanine metabolic process(GO:0006522) leucine metabolic process(GO:0006551) pyruvate family amino acid metabolic process(GO:0009078) leucine biosynthetic process(GO:0009098) response to amino acid(GO:0043200)
8.5 25.6 GO:0032978 protein insertion into membrane from inner side(GO:0032978)
8.4 25.1 GO:0019676 ammonia assimilation cycle(GO:0019676)
3.6 14.3 GO:0046040 IMP metabolic process(GO:0046040)
2.7 11.0 GO:1902600 aerobic electron transport chain(GO:0019646) hydrogen ion transmembrane transport(GO:1902600)
2.6 13.1 GO:0019521 D-gluconate metabolic process(GO:0019521) D-gluconate catabolic process(GO:0046177)
0.5 4.6 GO:0006855 drug transmembrane transport(GO:0006855)
0.4 2.1 GO:0071468 cellular response to acidic pH(GO:0071468)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
3.7 11.0 GO:0070069 cytochrome complex(GO:0070069)
0.5 52.8 GO:0030288 outer membrane-bounded periplasmic space(GO:0030288)
0.1 66.4 GO:0005829 cytosol(GO:0005829)
0.0 4.6 GO:0031226 intrinsic component of plasma membrane(GO:0031226)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
8.5 25.6 GO:0047451 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity(GO:0008693) 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity(GO:0019171) 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity(GO:0047451)
4.2 25.1 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors(GO:0016638)
2.7 11.0 GO:0048038 prenyltransferase activity(GO:0004659) quinone binding(GO:0048038) ubiquinone binding(GO:0048039)
0.7 2.1 GO:0051087 chaperone binding(GO:0051087)
0.7 44.8 GO:0043565 sequence-specific DNA binding(GO:0043565)
0.5 14.3 GO:0016879 ligase activity, forming carbon-nitrogen bonds(GO:0016879)
0.4 4.6 GO:0015238 drug transmembrane transporter activity(GO:0015238)
0.3 13.1 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor(GO:0016616)